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Kato A, Ohashi H. Quick Refolding of High-Concentration Proteins via Microchannel Dialysis. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c00410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aoi Kato
- Department of Chemical Engineering, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Hidenori Ohashi
- Department of Chemical Engineering, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
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2
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Hao M, Huang H, Hu Y, Qi H. Construction of a system for single-stranded DNA isolation. Biotechnol Lett 2020; 42:1663-1671. [DOI: 10.1007/s10529-020-02905-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/30/2020] [Indexed: 01/22/2023]
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Komarova N, Kuznetsov A. Inside the Black Box: What Makes SELEX Better? Molecules 2019; 24:E3598. [PMID: 31591283 PMCID: PMC6804172 DOI: 10.3390/molecules24193598] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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Schaub JM, Zhang H, Soniat MM, Finkelstein IJ. Assessing Protein Dynamics on Low-Complexity Single-Stranded DNA Curtains. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14882-14890. [PMID: 30044093 PMCID: PMC6679933 DOI: 10.1021/acs.langmuir.8b01812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-stranded DNA (ssDNA) is a critical intermediate in all DNA transactions. Because ssDNA is more flexible than double-stranded (ds) DNA, interactions with ssDNA-binding proteins (SSBs) may significantly compact or elongate the ssDNA molecule. Here, we develop and characterize low-complexity ssDNA curtains, a high-throughput single-molecule assay to simultaneously monitor protein binding and correlated ssDNA length changes on supported lipid bilayers. Low-complexity ssDNA is generated via rolling circle replication of short synthetic oligonucleotides, permitting control over the sequence composition and secondary structure-forming propensity. One end of the ssDNA is functionalized with a biotin, while the second is fluorescently labeled to track the overall DNA length. Arrays of ssDNA molecules are organized at microfabricated barriers for high-throughput single-molecule imaging. Using this assay, we demonstrate that E. coli SSB drastically and reversibly compacts ssDNA templates upon changes in NaCl concentration. We also examine the interactions between a phosphomimetic RPA and ssDNA. Our results indicate that RPA-ssDNA interactions are not significantly altered by these modifications. We anticipate that low-complexity ssDNA curtains will be broadly useful for single-molecule studies of ssDNA-binding proteins involved in DNA replication, transcription, and repair.
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Affiliation(s)
- Jeffrey M. Schaub
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
| | - Hongshan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
| | - Michael M. Soniat
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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Tolnai Z, Harkai Á, Szeitner Z, Scholz ÉN, Percze K, Gyurkovics A, Mészáros T. A simple modification increases specificity and efficiency of asymmetric PCR. Anal Chim Acta 2018; 1047:225-230. [PMID: 30567654 DOI: 10.1016/j.aca.2018.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/24/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
Although various methods have been developed to suffice the oligonucleotide demand of molecular biology laboratories, in vitro production of high-purity ssDNAs remains to be a challenging task. We hypothesized that complementing the asymmetric PCR with 3' phosphate blocked limiting primer decreases the mispriming thus reduces polymerisation of DNA by-products. The presented results attest our assumption that the primer blocked asymmetric PCR (PBA-PCR) selectively produces ssDNA of interest and is even suitable for effective amplification of DNA libraries of large sequence space. The high-throughput sequence analysis demonstrated that PBA-PCR also alleviates the PCR bias obstacle since it does not distort the sequence space. The practicability of the novel method was verified by monitoring the process of SELEX and screening of aptamer candidates using PBA-PCR produced ssDNAs in Amplified Luminescent Proximity Homogeneous Assay. In summary, we have developed a generally applicable method for straightforward, cost-effective production of ssDNA with on demand labelling.
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Affiliation(s)
- Zoltán Tolnai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary
| | - Ákos Harkai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary
| | - Zsuzsanna Szeitner
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary
| | - Éva Nagyné Scholz
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary
| | - Krisztina Percze
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary
| | - Anna Gyurkovics
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 37-47 Tűzoltó Street, Budapest, Hungary.
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Mazaafrianto DN, Maeki M, Ishida A, Tani H, Tokeshi M. Recent Microdevice-Based Aptamer Sensors. MICROMACHINES 2018; 9:E202. [PMID: 30424135 PMCID: PMC6187364 DOI: 10.3390/mi9050202] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 04/19/2018] [Accepted: 04/21/2018] [Indexed: 12/17/2022]
Abstract
Since the systematic evolution of ligands by exponential enrichment (SELEX) method was developed, aptamers have made significant contributions as bio-recognition sensors. Microdevice systems allow for low reagent consumption, high-throughput of samples, and disposability. Due to these advantages, there has been an increasing demand to develop microfluidic-based aptasensors for analytical technique applications. This review introduces the principal concepts of aptasensors and then presents some advanced applications of microdevice-based aptasensors on several platforms. Highly sensitive detection techniques, such as electrochemical and optical detection, have been integrated into lab-on-a-chip devices and researchers have moved towards the goal of establishing point-of-care diagnoses for target analyses.
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Affiliation(s)
- Donny Nugraha Mazaafrianto
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
| | - Masatoshi Maeki
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
| | - Akihiko Ishida
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
| | - Hirofumi Tani
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
| | - Manabu Tokeshi
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan.
- ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
- Innovative Research Center for Preventive Medical Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
- Institute of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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Heiat M, Ranjbar R, Latifi AM, Rasaee MJ, Farnoosh G. Essential strategies to optimize asymmetric PCR conditions as a reliable method to generate large amount of ssDNA aptamers. Biotechnol Appl Biochem 2017; 64:541-548. [PMID: 27222205 DOI: 10.1002/bab.1507] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/20/2016] [Indexed: 12/19/2022]
Abstract
Asymmetric PCR, a simple method to generate single-stranded DNA (ssDNA) aptamers in systematic evaluation of ligand by exponential enrichments rounds, is coupled with limitations. We investigated the essential strategies for optimization of conditions to perform a high-quality asymmetric PCR. Final concentrations of primers and template, the number of PCR cycles, and annealing temperature were selected as optimizing variables. The qualities of visualized PCR products were analyzed by ImageJ software. The highest proportion of interested DNA than unwanted products was considered as optimum conditions. Results revealed that the best values for primers ratio, final template concentration, annealing temperature, and PCR cycles were, respectively, 30:1, 1 ng/μL, 55 °C, and 20 cycles for the first and 50:1, 2 ng/μL, 59 °C, and 20 cycles for other rounds. No significant difference was found between optimized asymmetric PCR results in the rounds of two to eight (P > 0.05). The ssDNA quality in round 10 was significantly better than other rounds (P < 0.05). Generally, the ssDNA product with less dimers, double-stranded DNA (dsDNA), and smear are preferable. The dsDNA contamination is the worst, because it can act as antidote and inhibits aptameric performance. Therefore, to choose the best conditions, the lower amount of dsDNA is more important than other unwanted products.
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Affiliation(s)
- Mohammad Heiat
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mohammad Latifi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Farnoosh
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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[Letter to the Editor] NaOH concentration and streptavidin bead type are key factors for optimal DNA aptamer strand separation and isolation. Biotechniques 2016; 61:114-6. [PMID: 27625204 DOI: 10.2144/000114449] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/20/2016] [Indexed: 11/23/2022] Open
Abstract
Address correspondence to Geoffrey K. Kilili or Christine M. Karbiwnyk, Winchester Engineering and Analytical Center, US Food and Drug Administration, Winchester, MA, 01890. E-mail: Geoffrey.Kilili@fda.hhs.gov or Christine.Karbiwnyk@fda.hhs.gov.
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